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Above Iraq, a jet pilot notices a small disc of light that does not appear on his radar but moves erratically out of his line of sight. The Iraqi pilot contacts his base and requests identification of the object twenty-five miles away from him. However, the base personnel do not detect the object on their radar system and ask the pilot to confirm the object's bearings. When he looks for the object, the pilot cannot see it anywhere but mumbles that he did, a second ago. Suddenly, a bright light illuminates his cockpit, as the noise of an engine whizzes past him. The base personnel report he is under attack, moments before the object passes him again. The pilot attains a target lock on the object and fires a missile at it, causing it to erupt in a massive fireball. He reports he has hit the object.

In a NATO surveillance station on the Turkey/Iraq border in Hakkari, Turkey, soldiers sleeping in bunks hear a noise like an airplane falling as the light in the room momentarily darkens. When the soldiers hear a loud explosion outside, they rush to their feet. They hurry to look out a window to see a fiery explosion in a nearby wooded area. One soldier uses a radio to contact Red Crescent and reports a downed plane near the camp perimeter but a man's voice answers that Red Crescent is not currently detecting anything in the sky near the surveillance station. The soldier confirms the sighting and suggests Red Crescent have a medivac unit standing by, before he announces the soldiers are about to investigate the explosion. They leave the surveillance station as Red Crescent contacts Medivac One and reports the incident. Meanwhile, another small disc of light flies over the area and hovers above the crash site.

An exhausted truck driver, Ranheim, enters an area of heightened UFO activity in Tennessee, only to experience a power outage on his vehicle. He gets out to investigate. With shotgun and flashlight in hand, he heads towards the back of the truck. As he looks up and sees something in the sky, the back doors of the truck swing open and he fires repeatedly.

FBISpecial AgentsMulder and Scully rush to the incident scene. Scully suggests that, because of the long hours worked by the driver and the presence of a marsh nearby, the entire incident could merely have been a mix of tiredness, delirium and Swamp Gas, with the case therefore not being worthy of investigation. Mulder, however, detects radiation levels five times higher than background and crudely measures a slight temporal lag. The multiple sightings on the earlier night lead him to seek an interview with Ranheim.

At Lexington Police Station, Ranheim is being detained on the charge of firing a weapon on a county road. Mulder and Scully interview an exhausted Ranheim, who now reports having seen orange and green lights in the sky and a saucer-shaped craft, contrary to his previous report of seeing a "cigar-shaped and black" craft. He currently seems disinterested in telling his story and wants simply to leave. Since the incident the previous night, he has developed a cough, a fever and a rash. He admits to being an army veteran but claims never to have been in the Gulf when Scully suggests Gulf War Syndrome as a possible cause for his sudden illness. Police ChiefRivers releases Ranheim and sends Mulder and Scully on their way, wanting nothing to do with the case.

At the car rental office, Mulder suggests to Scully that someone had rattled Chief Rivers and that Ranheim was hiding something; at that same moment, a woman in the office asks to borrow Scully's pen for a moment. Mulder speculates that heightened UFO activity may be linked to Gulf War Syndrome, as soldiers report many UFOs during wartime and seeks "expert" advice.

Mulder takes Scully to meet the Lone Gunmen for the first time. After the agents listen dubiously to conversations regarding the Kennedy assassination, the true nature of the CIA and the real reasons for the magnetic stripes inside dollar bills, they discuss Gulf War Syndrome with the Lone Gunmen, who brand some of Mulder's ideas on the subject to be even wilder than their own.

Back at FBI Headquarters, Scully discovers the pen she lent out earlier at the car rental office is now bugged.

Mulder meets with Deep Throat, who passes him an envelope containing intercepted transmissions from Iraqi fighter jets who shot down a UFO, four days ago. As he leaves, Deep Throat tells Mulder he is on "a dangerous path." Scully discovers that the weight in the truck's manifest is about 2,000-pounds heavier than the records from three weigh-stations along the truck's route. She also finds that Ranheim's real name is Frank Druce, a member of Army Special Operations who did serve in Mosul, Iraq. Mulder hypothesizes that Druce was hired to escort the wreckage of a UFO and possibly an occupant to a laboratory in the United States, using the unmarked truck. Mulder and Scully decide to intercept the truck as it heads towards Colorado.

When Mulder returns home to collect some clothes for the trip, he discovers Deep Throat waiting for him in his house, with the apartment's main power switched off. Deep Throat gives Mulder a document which contains a photo taken at Fort Benning, Georgia, where seventeen UFOs were reported in a single hour, perhaps searching for the wreckage and occupant. As usual, Deep Throat dodges a direct question from Mulder and leaves him with more questions than answers.

Mulder falls for the photographic bait offered by Deep Throat and declares they should go immediately to Fort Benning. Scully examines the photo objectively and spots some minor lighting inconsistencies that reveal it to be a fake. After additional analysis by experts at the FBI, Mulder realizes they have been deceived by Deep Throat, a source Mulder had trusted completely.

When Mulder confronts Deep Throat about his deception, Deep Throat explains that there are some things Mulder shouldn't know, that he needed to throw him off the trail and that "a lie is most convincingly hidden between two truths." He denies responsibility for surveillance of Scully but infers that Mulder is being bugged too, a fact later confirmed when Mulder discovers a listening bug hidden within an electrical wall outlet in his apartment.

Upon arriving at McCarran Airport, Las Vegas, Nevada, Mulder and Scully make further inquiries, using public telephones to avoid their calls being traced and eavesdropped. They discover that the truck is heading west and hop on a flight to Seattle. They follow the truck for hours, then suddenly witness a bright light. The truck has stopped and Ranheim is missing. They open the truck and find, behind several boxes of auto-parts, a makeshift medical ward with a restraining stretcher and monitoring equipment. It is now empty, leading Mulder to believe they just witnessed a rescue mission.

The lack of empirical evidence, the normal levels of radiation and zero temporal lag lead Mulder to conclude it was a trick to further throw them off the scent.

Mulder liaises with friends at various UFO hotlines and discovers that the frequent sightings which followed the route of the truck have continued in the vicinity of Mattawa, Washington – around 100 miles from where the truck stopped. The two venture to Mattawa, where UFO party-goers tell them UFOs have been known to hover over the Hanford Power Plant. Mulder and Scully observe Ranheim exiting the power plant and use Lone Gunman Langly's expertise at hacking security systems, to provide forged IDs in order to access the facility.

Mulder and Scully are apprehended inside the facility. Mulder escapes custody and heads for the only area Langly could not get them access to: Level 6.

Level 6 appears to be an area for high-voltage research and a plethora of industrial electrical equipment is arranged around a quarantine cell. Mulder is quickly apprehended by armed guards, who are then dismissed by Deep Throat. Deep Throat informs Mulder the creature is dead, exterminated moments before by the government. He adds that this is standard international procedure and that he once carried out such an extermination himself, during the Vietnam War. Deep Throat reveals that the innocent and blank expression on the creature's face as he killed it haunts him to this day; this is why he comes to Mulder, so that one day, the truth might be known. As Mulder and Deep Throat separate, Scully rejoins her partner and the two are left wondering "which lie to believe."

Another of this episode's facets which was in the works over an extended duration was the concept of the Lone Gunmen. Glen Morgan saw a trio of men who became the basis for the fictional group at a UFO convention (which he attended with "Shapes" writer Marilyn Osborn) in June 1993, shortly before he and James Wong began writing for The X-Files. (The Truth Is Out There: The Official Guide to The X-Files, pp. 139-140) Morgan recounted, "I thought, 'Well, these people have got to make it in here somewhere.' It just took a long time to get them in." (Cinefantastique, Vol. 26/27, No. 6/1, p. 50)

This installment allowed Glen Morgan and James Wong a chance to write a Mythology episode, which they so wanted to do. The outing was inspired by fan writings. "A lot of that was from fan mail, what people wanted us to deal with," Glen Morgan recalled. (X-Files Confidential, p. 66) Part of the inspiration for this episode came specifically from messages posted by fans on the Internet. (Cinefantastique, Vol. 26/27, No. 6/1, p. 49) Morgan continued, "I think 'E.B.E.' was written for people who we felt were hardcore X-Files fans: people into UFOs and every conspiracy imaginable [....] The movie I kind of really looked at in order to catch the tone for 'E.B.E.' was All the President's Men, dealing with dark parking lots and that kind of paranoia." (X-Files Confidential, p. 66)

The first scene of this episode which Glen Morgan and James Wong wrote was the one in which Deep Throat claims to have killed an alien. (Starlog, issue #210, p. 63) The impetus for the scene was online fans who kept asking for more information on Deep Throat. Glen Morgan remembered, "We said, 'Why don't we finally give him a little backstory?' I said, 'I think it would be really cool if he admitted he had killed an alien.' And then we said, 'Well, he says he killed an alien. This guy, you never know whether he's lying or not, so let's leave it ambiguous,' and everyone on the computer will go, 'Is he lying or not?'" (Cinefantastique, Vol. 26/27, No. 6/1, p. 49)

Glen Morgan and James Wong arranged this episode so its structure centered on a line of dialogue from Deep Throat. Morgan explained, "The whole thing was written to get to the line, 'A lie is best hidden between two truths.' We worked the whole thing to get to that." Morgan noted the line was representative of the way in which installments of The X-Files were typically written, taking a variety of facts from a scientific magazine or book and adding some fiction into the mix. (Cinefantastique, Vol. 26/27, No. 6/1, p. 49)

This episode's script went through four drafts. These were dated 11th, 18th, 20th and 24th January 1994.

Executives at Fox expressed a lot of opposition to this episode. They particularly protested against its depiction of Deep Throat, believing he was a stock character who shouldn't be explored by the writers and who should simply be used to feed information to Mulder. Glen Morgan and Executive Producer Chris Carter showed the executives the same kind of online comments which had sparked Deep Throat's development here, which convinced Fox to leave the storyline alone. (Sci-Fi Universe, issue #10, p. 35)

The power plant that appears near the end of this episode was depicted using two locations. The exterior was Triumf, at 4004 Wesbrook Mall, University of British Columbia (UBC), Vancouver, whereas the interior was inside BC Hydro's Powertech at 12388 88 Avenue, Surrey. (X Marks the Spot (On Location with The X-Files), p. 44)

This is the second of two first season installments of The X-Files which were directed by William Graham, the first having been "Space". About "E.B.E.", he remarked, "I got involved in this episode because they liked the first show I did." (TV Zone, issue 83, p. 14)

For the filming of a shot showing Mulder and Scully as they board a bus to Washington prior to meeting with the Lone Gunmen, the camera followed David Duchovny and Gillian Anderson onto the bus. "We actually followed them using a radio microphone," explained William Graham. "We took them to their seats and kept filming as the bus drove away [....] It was an innovative type of shot." (TV Zone, issue 83, p. 14)

The scene in which Byers dismantles a US$20 bill was difficult to get right, as the actors kept doing it wrong. Bruce Hardwood recalled, "The props man came up to me. 'These are the twenty dollar bills. You've only got ten chances.'" Laughing, Glen Morgan estimated that, in trying to perform the scene properly, "probably about a hundred and twenty dollars were destroyed." ("Behind the Truth: Lone Gunmen", TXF Season 1 DVD special features)

Some things were constructed specially for this installment. "We built a couple of things," noted Art Director Graeme Murray. These included the room which appears to be a kind of life-support area for an extraterrestrial. Only a small fraction of what was built of the room was shown on camera. (X-Files Confidential, p. 67)

When Mulder and Scully enter the Hanford Power Plant using aliases, Mulder says his name is Tom Braidwood and Scully uses the name Val Stefoff. In reality, both Tom Braidwood and Vladimir Stefoff were First Assistant Directors of The X-Files, with Braidwood additionally appearing as Melvin Frohike.

This is the first of only two episodes in Season 1 that feature scenes set in both Mulder and Scully's apartments, the second episode being "The Erlenmeyer Flask".

Following their initial appearance in this episode, Frohike, Langly and Byers became recurring characters in The X-Files, even eventually spawning their own spin-off series. Also introduced here were the notions of Frohike being characterized as perverted and having a crush on Scully. "That all resulted from the first episode where my line was 'She's hot,'" commented Tom Braidwood, "which destined me to being a lech for the rest of my career." (The Complete X-Files: Behind the Series, the Myths and the Movies, p. 49)

Glen Morgan was unhappy with the initial appearance of the Lone Gunmen, suspecting he and his writing partner James Wong had made a mistake in executing the character concept, unaware the Gunmen would prove popular. As Morgan later recalled, "We had kind of written them off." (The Truth Is Out There: The Official Guide to The X-Files, p. 140)

James Wong was left disappointed with this installment. He complained, "I really felt we didn't do a great job on the script [....] At the end I felt like we didn't really gain a lot of new ground or learn a lot of new things. I think we played a lot of texture instead of substance." (X-Files Confidential, p. 66)

William Graham described the shot of Mulder and Scully boarding a bus as "interesting" and a shot "which everyone liked." (TV Zone, issue 83, p. 14)

Chris Carter held this outing in high regard. "I thought it was well directed by Bill Graham," he specified. "I thought there were some really memorable scenes in it, particularly Deep Throat and the shark tank, also the teaser with the Iraqi pilot. Some really wacky stuff: the UFO party, and the introduction of the Lone Gunmen." (X-Files Confidential, p. 66) Other scenes Carter found notable were the night-time one in which Deep Throat and Mulder sit in Washington and the scene where Mulder and Scully discover an abandoned medical laboratory in the back of a truck. Carter referred to the conversation between Mulder and Deep Throat in the former scene as "a very sort of interesting discussion," and said of the latter scene, "I just thought that it was so creepy [....] It was, I don't know, it's a very strange scene and kind of creepy and wonderful, and it led to the finding of a similar kind of operation at the ending of the show, a nice little bookending of those elements. A very successful episode, I think, overall and we didn't see an alien during the show, which was the amazing thing; we only suggested that, in fact, one was in that truck at some point." Carter believed this episode was good for how it developed the character of Deep Throat in general. "I think it helps to take his character in an interesting direction, which is to make him as much a man who can be trusted as sometimes mistrusted." ("Chris Carter Talks About Season One Episodes: E.B.E.", TXF Season 1 DVD special features)

This episode achieved a Nielsen household rating of 6.2, with an audience share of 9. This means that roughly 6.2 percent of all television-equipped households, and 9 percent of households watching television, were tuned in to the episode. It was viewed by 5.8 million households. (The Truth Is Out There: The Official Guide to The X-Files, p. 248)

Audience reaction to this episode seemed to long for the presence of Eugene Victor Tooms. "They screened 'E.B.E.'," recalled Glen Morgan, "and people were saying, 'I like the UFO episodes, but there was one where this guy kind of stretched…'" Morgan found this viewer response frustrating, considering that a test screening of "Squeeze" had conversely seemed to indicate an interest in the Mythology episodes. Despite the apparent lukewarm nature of the initial reception to this installment, Chris Carter called it one "of our most popular first-season episodes." (X-Files Confidential, p. 66) Likewise, Glen Morgan and James Wong thought the Lone Gunmen had essentially been a failure only until the producers became aware that fans on the internet were responding favorably to the trio of characters; the response eventually led to the reappearances of the Lone Gunmen. (The Truth Is Out There: The Official Guide to The X-Files, p. 140)

Cinefantastique (Vol. 26/27, No. 6/1, p. 49) scores this episode 4 out of 4 stars and remarks the episode contains "notable performances all around for the trio of Duchovny, Anderson and Hardin, whether they are delivering some of Morgan and Wong's deadpan humor or agonizing over the latest turn of events."

The X-Files Magazine Yearbook 2002 (p. 66) highlights the scene in which Mulder assures Scully he suspects it is "remotely plausible" for someone to think she is "hot" as one of their twenty most romantic scenes in the entire series.

In his reference bookWanting to Believe: A Critical Guide to The X-Files, Millennium and The Lone Gunmen, writer Robert Shearman rated this episode 4 out of 5 stars. He found the installment "deliberately frustrating" and stated, "Is there any episode in which the theme of the programme, its conspiracy and paranoia and deceit, are better summed up or handled so deftly? [....] 'E.B.E.' [...] risks coming off as very cold and very schematic. It's like an Escher print – there's no beginning, and no end, because for all the characters' search for a truth, there's no simple truth we can seize upon to expose the lies surrounding it." He also described the outing as "a marvellous slice of paranoia." Shearman particularly praised how it makes use of Deep Throat and the Lone Gunmen. He called the latter's appearance "a scene of great comedy to enjoy" but noted that the episode's focus on paranoia "gives them ironically a sense of importance and esteem they don't deserve." He went on to say, "It's why, perhaps, for all its obvious cleverness, 'E.B.E.' still strikes me as vaguely dissatisfying – as if, underneath, it knows that all the intrigue and subterfuge The X-Files are playing with here are masks for a rather hollow centre. If so, it's an interesting critique of the show [....] 'E.B.E.', as good as it is, leaves an odd taste in the mouth."

As this episode was originally planned to be the only appearance of the Lone Gunmen, First Assistant Director Tom Braidwood ended up portraying Frohike, since his part was thought to be merely a one-shot deal. He only had two short lines, after all. ("Bond, Jimmy Bond" audio commentary, TLG Season 1 DVD special features)